S-Palmitoylation is a reversible lipid post-translational modification that has been observed on mitochondrial proteins, but both the regulation and functional consequences of mitochondrial S-palmitoylation are poorly understood. Here, we show that perturbing the ‘erasers’ of S-palmitoylation, acyl protein thioesterases (APTs), with either pan-active inhibitors or a mitochondrial-targeted APT inhibitor, diminishes the antioxidant buffering capacity of mitochondria. Surprisingly, this effect was not mediated by the only known mitochondrial APT, but rather by a resident mitochondrial protein with no known endogenous function, ABHD10. We show that ABHD10 is a member of the APT family of regulatory proteins and identify peroxiredoxin-5 (PRDX5), a key antioxidant protein, as a target of ABHD10 S-depalmitoylase activity. We then find that ABHD10 regulates the S-palmitoylation status of the nucleophilic active site residue of PRDX5, providing a direct mechanistic connection between ABHD10-mediated S-depalmitoylation of PRDX5 and its antioxidant capacity.
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All structural data have been deposited in the Protein Data Bank (PDB: 6NY9). Additional data supporting the findings of this manuscript are available from the corresponding author upon reasonable request.
Blanc, M. et al. SwissPalm: protein palmitoylation database. F1000Res. 4, 261 (2015).
Lanyon-Hogg, T., Faronato, M., Serwa, R. A. & Tate, E. W. Dynamic protein acylation: new substrates, mechanisms, and drug targets. Trends Biochem. Sci. 42, 566–581 (2017).
Martin, B. R., Wang, C., Adibekian, A., Tully, S. E. & Cravatt, B. F. Global profiling of dynamic protein palmitoylation. Nat. Methods 9, 84–89 (2011).
Dekker, F. J. et al. Small-molecule inhibition of APT1 affects Ras localization and signaling. Nat. Chem. Biol. 6, 449–456 (2010).
Brownlee, C. & Heald, R. Importin α partitioning to the plasma membrane regulates intracellular scaling. Cell 176, 805–815.e8 (2019).
Chan, P. et al. Autopalmitoylation of TEAD proteins regulates transcriptional output of the Hippo pathway. Nat. Chem. Biol. 12, 282–289 (2016).
Chen, S. et al. Palmitoylation-dependent activation of MC1R prevents melanomagenesis. Nature 549, 399–403 (2017).
Ko, P. J. & Dixon, S. J. Protein palmitoylation and cancer. EMBO Rep. 19, e46666 (2018).
Zareba-Koziol, M., Figiel, I., Bartkowiak-Kaczmarek, A. & Wlodarczyk, J. Insights into protein S-palmitoylation in synaptic plasticity and neurological disorders: potential and limitations of methods for detection and analysis. Front. Mol. Neurosci. 11, 175 (2018).
Sobocinska, J., Roszczenko-Jasinska, P., Ciesielska, A. & Kwiatkowska, K. Protein palmitoylation and its role in bacterial and viral infections. Front. Immunol. 8, 2003 (2018).
Gottlieb, C. D. & Linder, M. E. Structure and function of DHHC protein S-acyltransferases. Biochem. Soc. Trans. 45, 923–928 (2017).
Duncan, J. A. & Gilman, A. G. A cytoplasmic acyl-protein thioesterase that removes palmitate from G protein α subunits and p21RAS. J. Biol. Chem. 273, 15830–15837 (1998).
Lin, D. T. & Conibear, E. ABHD17 proteins are novel protein depalmitoylases that regulate N-Ras palmitate turnover and subcellular localization. eLife 4, e11306 (2015).
Long, J. Z. & Cravatt, B. F. The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem. Rev. 111, 6022–6063 (2011).
Yokoi, N. et al. Identification of PSD-95 depalmitoylating enzymes. J. Neurosci. 36, 6431–6444 (2016).
Kostiuk, M. A. et al. Identification of palmitoylated mitochondrial proteins using a bio-orthogonal azido-palmitate analogue. FASEB J. 22, 721–732 (2008).
Tang, M., Lu, L., Huang, Z. & Chen, L. Palmitoylation signaling: a novel mechanism of mitochondria dynamics and diverse pathologies. Acta Biochim. Biophys. Sin. (Shanghai) 50, 831–833 (2018).
Maynard, T. M. et al. Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes. Mol. Cell Neurosci. 39, 439–451 (2008).
Shen, L. F. et al. Role of S-palmitoylation by ZDHHC13 in mitochondrial function and metabolism in liver. Sci. Rep. 7, 2182 (2017).
Kathayat, R. S. et al. Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes. Nat. Commun. 9, 334 (2018).
Kathayat, R. S. & Dickinson, B. C. Measuring S-depalmitoylation activity in vitro and in live cells with fluorescent probes. Methods Mol. Biol. 2009, 99–109 (2019).
Knoops, B., Goemaere, J., Van der Eecken, V. & Declercq, J. P. Peroxiredoxin 5: structure, mechanism, and function of the mammalian atypical 2-Cys peroxiredoxin. Antioxid. Redox Signal. 15, 817–829 (2011).
Frohlich, M., Dejanovic, B., Kashkar, H., Schwarz, G. & Nussberger, S. S-palmitoylation represents a novel mechanism regulating the mitochondrial targeting of BAX and initiation of apoptosis. Cell Death Dis. 5, e1057 (2014).
Zorov, D. B., Juhaszova, M. & Sollott, S. J. Mitochondrial reactive oxygen species (ROS) and ROS-induced ROS release. Physiol. Rev. 94, 909–950 (2014).
Thinon, E., Fernandez, J. P., Molina, H. & Hang, H. C. Selective enrichment and direct analysis of protein S-palmitoylation sites. J. Proteome Res. 17, 1907–1922 (2018).
Dickinson, B. C. & Chang, C. J. A targetable fluorescent probe for imaging hydrogen peroxide in the mitochondria of living cells. J. Am. Chem. Soc. 130, 9638–9639 (2008).
Rhee, S. G. & Kil, I. S. Multiple functions and regulation of mammalian peroxiredoxins. Annu. Rev. Biochem. 86, 749–775 (2017).
Wan, J., Roth, A. F., Bailey, A. O. & Davis, N. G. Palmitoylated proteins: purification and identification. Nat. Protoc. 2, 1573–1584 (2007).
Martin, B. R. & Cravatt, B. F. Large-scale profiling of protein palmitoylation in mammalian cells. Nat. Methods 6, 135–138 (2009).
Kathayat, R. S., Elvira, P. D. & Dickinson, B. C. A fluorescent probe for cysteine depalmitoylation reveals dynamic APT signaling. Nat. Chem. Biol. 13, 150–152 (2017).
Zielonka, J. et al. Mitochondria-targeted triphenylphosphonium-based compounds: syntheses, mechanisms of action, and therapeutic and diagnostic applications. Chem. Rev. 117, 10043–10120 (2017).
Qiu, T., Kathayat, R. S., Cao, Y., Beck, M. W. & Dickinson, B. C. A fluorescent probe with improved water solubility permits the analysis of protein S-depalmitoylation activity in live cells. Biochemistry 57, 221–225 (2018).
Adibekian, A. et al. Confirming target engagement for reversible inhibitors in vivo by kinetically tuned activity-based probes. J. Am. Chem. Soc. 134, 10345–10348 (2012).
Won, S. J. et al. Molecular mechanism for isoform-selective inhibition of acyl protein thioesterases 1 and 2 (APT1 and APT2). ACS Chem. Biol. 11, 3374–3382 (2016).
Rhee, H. W. et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 339, 1328–1331 (2013).
Ito, Y., Fukami, T., Yokoi, T. & Nakajima, M. An orphan esterase ABHD10 modulates probenecid acyl glucuronidation in human liver. Drug Metab. Dispos. 42, 2109–2116 (2014).
Iwamura, A., Fukami, T., Higuchi, R., Nakajima, M. & Yokoi, T. Human alpha/beta hydrolase domain containing 10 (ABHD10) is responsible enzyme for deglucuronidation of mycophenolic acid acyl-glucuronide in liver. J. Biol. Chem. 287, 9240–9249 (2012).
Dickinson, B. C., Huynh, C. & Chang, C. J. A palette of fluorescent probes with varying emission colors for imaging hydrogen peroxide signaling in living cells. J. Am. Chem. Soc. 132, 5906–5915 (2010).
Devedjiev, Y., Dauter, Z., Kuznetsov, S. R., Jones, T. L. & Derewenda, Z. S. Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 Å. Structure 8, 1137–1146 (2000).
Castello, P. R., Drechsel, D. A. & Patel, M. Mitochondria are a major source of paraquat-induced reactive oxygen species production in the brain. J. Biol. Chem. 282, 14186–14193 (2007).
McDonald, C., Muhlbauer, J., Perlmutter, G., Taparra, K. & Phelan, S. A. Peroxiredoxin proteins protect MCF-7 breast cancer cells from doxorubicin-induced toxicity. Int. J. Oncol. 45, 219–226 (2014).
Sugimoto, H., Hayashi, H. & Yamashita, S. Purification, cDNA cloning, and regulation of lysophospholipase from rat liver. J. Biol. Chem. 271, 7705–7711 (1996).
Sadeghi, R. S. et al. Wnt5a signaling induced phosphorylation increases APT1 activity and promotes melanoma metastatic behavior. eLife 7, e34362 (2018).
Amara, N., Foe, I. T., Onguka, O., Garland, M. & Bogyo, M. Synthetic fluorogenic peptides reveal dynamic substrate specificity of depalmitoylases. Cell Chem. Biol. 26, 35–47.e7 (2019).
Zuhl, A. M. et al. Competitive activity-based protein profiling identifies aza-beta-lactams as a versatile chemotype for serine hydrolase inhibition. J. Am. Chem. Soc. 134, 5068–5071 (2012).
Parvez, S., Long, M. J. C., Poganik, J. R. & Aye, Y. Redox signaling by reactive electrophiles and oxidants. Chem. Rev. 118, 8798–8888 (2018).
Corvi, M. M., Soltys, C. L. & Berthiaume, L. G. Regulation of mitochondrial carbamoyl-phosphate synthetase 1 activity by active site fatty acylation. J. Biol. Chem. 276, 45704–45712 (2001).
Garland, M. et al. Development of an activity-based probe for acyl-protein thioesterases. PLoS One 13, e0190255 (2018).
Liu, Y., Patricelli, M. P. & Cravatt, B. F. Activity-based protein profiling: the serine hydrolases. Proc. Natl Acad. Sci. USA 96, 14694–14699 (1999).
Ogasawara, D. et al. Selective blockade of the lyso-PS lipase ABHD12 stimulates immune responses in vivo. Nat. Chem. Biol. 14, 1099–1108 (2018).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Peng, J. & Xu, J. RaptorX: exploiting structure information for protein alignment by statistical inference. Proteins 79, 161–171 (2011).
Kallberg, M. et al. Template-based protein structure modeling using the RaptorX web server. Nat. Protoc. 7, 1511–1522 (2012).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
Hsu, C. Y. & Uludag, H. A simple and rapid nonviral approach to efficiently transfect primary tissue-derived cells using polyethylenimine. Nat. Protoc. 7, 935–945 (2012).
Buttke, T. M., McCubrey, J. A. & Owen, T. C. Use of an aqueous soluble tetrazolium/formazan assay to measure viability and proliferation of lymphokine-dependent cell lines. J. Immunol. Methods 157, 233–240 (1993).
Lin, T. K. et al. Specific modification of mitochondrial protein thiols in response to oxidative stress: a proteomics approach. J. Biol. Chem. 277, 17048–17056 (2002).
This work was supported by the University of Chicago, the National Institute of General Medical Sciences of the National Institutes of Health (R35 GM119840, to B.C.D.) and a ‘Catalyst Award’ (to B.C.D.) from the Chicago Biomedical Consortium, with support from the Searle Funds at The Chicago Community Trust. The crystallographic work is based on research conducted at the Advanced Photon Source on the Northeastern Collaborative Access Team beamline, 24-ID-C, which is supported by a grant from the National Institute of General Medical Sciences (P41 GM103403) from the National Institutes of Health. This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. We thank the staff of the Advanced Photon Source at Argonne National Laboratory for providing technical advice during data collection, L. Hu (University of Chicago) for providing advice on crystal growth, D. Koirala (University of Chicago) for assistance with X-ray diffraction data collection, Y. Shao (University of Chicago) for advice on structure refinement and S. Ahmadiantehrani (University of Chicago) for assistance proofing the manuscript.
B.C.D. and R.S.K. have a patent (US20180147250A1) on the DPPs.
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Cao, Y., Qiu, T., Kathayat, R.S. et al. ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5. Nat Chem Biol 15, 1232–1240 (2019). https://doi.org/10.1038/s41589-019-0399-y
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